| Sample | Total_before | R1_before | R1_before_length | R2_before | R2_before_length | GC_before | Total_after | R1_after | R1_after_length | R2_after | R2_after_length | GC_after | Reads_discarded |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| test3 | 16000 | 8000 | 301 | 8000 | 301 | 0.44 | 15236 | 7618 | 300 | 7618 | 300 | 0.44 | 764 |
| test1 | 16000 | 8000 | 301 | 8000 | 301 | 0.48 | 14954 | 7477 | 300 | 7477 | 300 | 0.48 | 1046 |
| test5 | 16000 | 8000 | 301 | 8000 | 301 | 0.46 | 15194 | 7597 | 300 | 7597 | 300 | 0.46 | 806 |
| test6 | 16000 | 8000 | 301 | 8000 | 301 | 0.46 | 15052 | 7526 | 300 | 7526 | 300 | 0.46 | 948 |
| test2 | 16000 | 8000 | 301 | 8000 | 301 | 0.48 | 14702 | 7351 | 300 | 7351 | 300 | 0.48 | 1298 |
| test4 | 16000 | 8000 | 301 | 8000 | 301 | 0.46 | 15056 | 7528 | 300 | 7528 | 300 | 0.46 | 944 |
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(shannonaov)
## W = 0.96378, p-value = 0.8483
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 2.3696, df = 1, p-value = 0.1237
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.0186 0.01863 0.16 0.709
## Residuals 4 0.4645 0.11612
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.1114473 -0.883944 0.6610495 0.709219
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(simpsonaov)
## W = 0.97915, p-value = 0.9473
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 1.1591, df = 1, p-value = 0.2817
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.0034 0.0034 0.085 0.785
## Residuals 4 0.1604 0.0401
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.04762309 -0.5015975 0.4063513 0.7853334
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(richaov)
## W = 0.88042, p-value = 0.271
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 0.092238, df = 1, p-value = 0.7614
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.3181 0.3181 1.48 0.291
## Residuals 4 0.8598 0.2150
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = richdata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.4605252 -1.511576 0.5905262 0.2906586
##
##
## --------------------------------------------------------------
##
## Call:
## adonis(formula = bray.distance ~ data5$treatment)
##
## Permutation: free
## Number of permutations: 719
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## data5$treatment 1 1.07522 1.07522 7.6237 0.65588 0.1
## Residuals 4 0.56415 0.14104 0.34412
## Total 5 1.63937 1.00000
## Run 0 stress 8.516666e-05
## Run 1 stress 0
## ... New best solution
## ... Procrustes: rmse 0.2292647 max resid 0.3555478
## Run 2 stress 0.1420473
## Run 3 stress 0
## ... Procrustes: rmse 0.0763136 max resid 0.09339155
## Run 4 stress 9.015944e-05
## ... Procrustes: rmse 0.04246819 max resid 0.05812314
## Run 5 stress 0.2269841
## Run 6 stress 0.1420473
## Run 7 stress 0
## ... Procrustes: rmse 0.1570328 max resid 0.3247846
## Run 8 stress 0
## ... Procrustes: rmse 0.125224 max resid 0.2303329
## Run 9 stress 7.999405e-05
## ... Procrustes: rmse 0.2224407 max resid 0.38638
## Run 10 stress 0.2269841
## Run 11 stress 0.1420473
## Run 12 stress 0
## ... Procrustes: rmse 0.118559 max resid 0.220027
## Run 13 stress 0.1420473
## Run 14 stress 0
## ... Procrustes: rmse 0.04684244 max resid 0.0688851
## Run 15 stress 9.885943e-05
## ... Procrustes: rmse 0.0678611 max resid 0.09331432
## Run 16 stress 8.206816e-05
## ... Procrustes: rmse 0.1550841 max resid 0.3075236
## Run 17 stress 9.34972e-05
## ... Procrustes: rmse 0.2065033 max resid 0.4214932
## Run 18 stress 0
## ... Procrustes: rmse 0.126147 max resid 0.1994897
## Run 19 stress 0
## ... Procrustes: rmse 0.1130878 max resid 0.1824697
## Run 20 stress 0.1420473
## Run 21 stress 0
## ... Procrustes: rmse 0.1485547 max resid 0.2519089
## Run 22 stress 0
## ... Procrustes: rmse 0.1212342 max resid 0.2154881
## Run 23 stress 0.2181459
## Run 24 stress 8.200665e-05
## ... Procrustes: rmse 0.2143283 max resid 0.429963
## Run 25 stress 0.2181459
## Run 26 stress 0
## ... Procrustes: rmse 0.1002697 max resid 0.1923843
## Run 27 stress 0
## ... Procrustes: rmse 0.1041719 max resid 0.1422895
## Run 28 stress 0.2269841
## Run 29 stress 6.245777e-05
## ... Procrustes: rmse 0.1383498 max resid 0.2163295
## Run 30 stress 0.2029041
## Run 31 stress 0
## ... Procrustes: rmse 0.1241107 max resid 0.2182096
## Run 32 stress 0
## ... Procrustes: rmse 0.07906875 max resid 0.1253994
## Run 33 stress 0
## ... Procrustes: rmse 0.1103616 max resid 0.1687388
## Run 34 stress 2.042108e-06
## ... Procrustes: rmse 0.1339719 max resid 0.2333751
## Run 35 stress 9.74567e-05
## ... Procrustes: rmse 0.1284 max resid 0.1859043
## Run 36 stress 0
## ... Procrustes: rmse 0.07798043 max resid 0.1214119
## Run 37 stress 0
## ... Procrustes: rmse 0.1092728 max resid 0.1734401
## Run 38 stress 4.775983e-05
## ... Procrustes: rmse 0.2000035 max resid 0.4095928
## Run 39 stress 3.886002e-05
## ... Procrustes: rmse 0.1248505 max resid 0.2148006
## Run 40 stress 0
## ... Procrustes: rmse 0.1352201 max resid 0.2162602
## Run 41 stress 0
## ... Procrustes: rmse 0.1262112 max resid 0.1885194
## Run 42 stress 5.339001e-05
## ... Procrustes: rmse 0.2083404 max resid 0.3574877
## Run 43 stress 0.2029041
## Run 44 stress 0.1420473
## Run 45 stress 0
## ... Procrustes: rmse 0.102437 max resid 0.1498367
## Run 46 stress 5.22987e-05
## ... Procrustes: rmse 0.1817013 max resid 0.3806718
## Run 47 stress 0
## ... Procrustes: rmse 0.1315114 max resid 0.1869779
## Run 48 stress 0
## ... Procrustes: rmse 0.1296647 max resid 0.1929563
## Run 49 stress 0
## ... Procrustes: rmse 0.1016486 max resid 0.1490199
## Run 50 stress 0.2181459
## Run 51 stress 0
## ... Procrustes: rmse 0.1666925 max resid 0.2812047
## Run 52 stress 0
## ... Procrustes: rmse 0.04865803 max resid 0.07450743
## Run 53 stress 0.2181459
## Run 54 stress 0
## ... Procrustes: rmse 0.1072679 max resid 0.1833416
## Run 55 stress 9.402591e-05
## ... Procrustes: rmse 0.1652184 max resid 0.2871537
## Run 56 stress 0
## ... Procrustes: rmse 0.2055956 max resid 0.3592358
## Run 57 stress 0
## ... Procrustes: rmse 0.09122371 max resid 0.1355847
## Run 58 stress 0.2181459
## Run 59 stress 0
## ... Procrustes: rmse 0.07966123 max resid 0.1270126
## Run 60 stress 0.2269841
## Run 61 stress 0
## ... Procrustes: rmse 0.06335752 max resid 0.09949353
## Run 62 stress 0
## ... Procrustes: rmse 0.1554245 max resid 0.2581932
## Run 63 stress 0.2181459
## Run 64 stress 0.2029041
## Run 65 stress 0
## ... Procrustes: rmse 0.1185207 max resid 0.1752303
## Run 66 stress 4.042124e-05
## ... Procrustes: rmse 0.2143988 max resid 0.432039
## Run 67 stress 0
## ... Procrustes: rmse 0.08432112 max resid 0.131646
## Run 68 stress 0.2181459
## Run 69 stress 9.688414e-05
## ... Procrustes: rmse 0.1926112 max resid 0.3977367
## Run 70 stress 8.291099e-05
## ... Procrustes: rmse 0.2189258 max resid 0.3867534
## Run 71 stress 9.960685e-05
## ... Procrustes: rmse 0.2237682 max resid 0.4312248
## Run 72 stress 3.088143e-05
## ... Procrustes: rmse 0.07400363 max resid 0.1026921
## Run 73 stress 0.2269841
## Run 74 stress 0.2181459
## Run 75 stress 0.1420473
## Run 76 stress 0
## ... Procrustes: rmse 0.0777429 max resid 0.1083593
## Run 77 stress 0.1420473
## Run 78 stress 0
## ... Procrustes: rmse 0.09935545 max resid 0.1493743
## Run 79 stress 0.2181459
## Run 80 stress 0
## ... Procrustes: rmse 0.08612822 max resid 0.1408433
## Run 81 stress 9.791028e-05
## ... Procrustes: rmse 0.2055398 max resid 0.4106227
## Run 82 stress 0.1420473
## Run 83 stress 0.2181459
## Run 84 stress 0
## ... Procrustes: rmse 0.08166741 max resid 0.1198376
## Run 85 stress 0
## ... Procrustes: rmse 0.1021789 max resid 0.1732992
## Run 86 stress 0
## ... Procrustes: rmse 0.09787576 max resid 0.1472266
## Run 87 stress 0
## ... Procrustes: rmse 0.113549 max resid 0.1834908
## Run 88 stress 9.772695e-05
## ... Procrustes: rmse 0.2057312 max resid 0.3518287
## Run 89 stress 0
## ... Procrustes: rmse 0.1328987 max resid 0.2023825
## Run 90 stress 0.2159914
## Run 91 stress 0
## ... Procrustes: rmse 0.08548373 max resid 0.1061624
## *** No convergence -- monoMDS stopping criteria:
## 63: stress < smin
## 11: stress ratio > sratmax
## 17: scale factor of the gradient < sfgrmin
## [1] "No Convergence"
## Run 0 stress 3.864101e-05
## Run 1 stress 9.618523e-05
## ... Procrustes: rmse 0.08265051 max resid 0.09880757
## Run 2 stress 9.674701e-05
## ... Procrustes: rmse 0.09964885 max resid 0.122559
## Run 3 stress 6.775705e-06
## ... New best solution
## ... Procrustes: rmse 0.169141 max resid 0.2281253
## Run 4 stress 0
## ... New best solution
## ... Procrustes: rmse 0.1467183 max resid 0.2523122
## Run 5 stress 6.833422e-05
## ... Procrustes: rmse 0.1648122 max resid 0.2214621
## Run 6 stress 0
## ... Procrustes: rmse 0.2357521 max resid 0.3990029
## Run 7 stress 0
## ... Procrustes: rmse 0.1903864 max resid 0.2834956
## Run 8 stress 6.002245e-05
## ... Procrustes: rmse 0.1519616 max resid 0.2161842
## Run 9 stress 9.487699e-05
## ... Procrustes: rmse 0.1590915 max resid 0.2205284
## Run 10 stress 9.662979e-05
## ... Procrustes: rmse 0.1765616 max resid 0.2739234
## Run 11 stress 0
## ... Procrustes: rmse 0.1796174 max resid 0.2625688
## Run 12 stress 0
## ... Procrustes: rmse 0.07320751 max resid 0.1208306
## Run 13 stress 0
## ... Procrustes: rmse 0.0726035 max resid 0.104632
## Run 14 stress 0
## ... Procrustes: rmse 0.1537718 max resid 0.2466778
## Run 15 stress 0
## ... Procrustes: rmse 0.1827372 max resid 0.2756763
## Run 16 stress 8.77228e-05
## ... Procrustes: rmse 0.1231251 max resid 0.2167976
## Run 17 stress 9.589444e-05
## ... Procrustes: rmse 0.177905 max resid 0.2551409
## Run 18 stress 0
## ... Procrustes: rmse 0.2317487 max resid 0.3978466
## Run 19 stress 9.754167e-05
## ... Procrustes: rmse 0.2134792 max resid 0.352959
## Run 20 stress 0
## ... Procrustes: rmse 0.1380613 max resid 0.2526259
## Run 21 stress 0
## ... Procrustes: rmse 0.2264863 max resid 0.4021794
## Run 22 stress 0
## ... Procrustes: rmse 0.08355771 max resid 0.1584266
## Run 23 stress 0
## ... Procrustes: rmse 0.1980071 max resid 0.2980975
## Run 24 stress 4.892489e-05
## ... Procrustes: rmse 0.2425368 max resid 0.4394601
## Run 25 stress 0
## ... Procrustes: rmse 0.1088582 max resid 0.183734
## Run 26 stress 0
## ... Procrustes: rmse 0.1762248 max resid 0.2120584
## Run 27 stress 0
## ... Procrustes: rmse 0.2065393 max resid 0.3882593
## Run 28 stress 0.1512494
## Run 29 stress 8.913664e-05
## ... Procrustes: rmse 0.157248 max resid 0.2302327
## Run 30 stress 9.861122e-05
## ... Procrustes: rmse 0.1827239 max resid 0.2727363
## Run 31 stress 5.403868e-05
## ... Procrustes: rmse 0.2284711 max resid 0.3857031
## Run 32 stress 0
## ... Procrustes: rmse 0.08806296 max resid 0.1562183
## Run 33 stress 0
## ... Procrustes: rmse 0.2039279 max resid 0.2769838
## Run 34 stress 9.690529e-05
## ... Procrustes: rmse 0.1640622 max resid 0.2358574
## Run 35 stress 1.601223e-05
## ... Procrustes: rmse 0.1083471 max resid 0.1393038
## Run 36 stress 9.75765e-05
## ... Procrustes: rmse 0.1679021 max resid 0.2425338
## Run 37 stress 0
## ... Procrustes: rmse 0.1317383 max resid 0.223774
## Run 38 stress 0
## ... Procrustes: rmse 0.1073714 max resid 0.1490398
## Run 39 stress 9.540333e-05
## ... Procrustes: rmse 0.1226659 max resid 0.2115139
## Run 40 stress 8.011839e-05
## ... Procrustes: rmse 0.08216674 max resid 0.1055457
## Run 41 stress 0
## ... Procrustes: rmse 0.1466075 max resid 0.2236215
## Run 42 stress 9.880402e-05
## ... Procrustes: rmse 0.167597 max resid 0.2446863
## Run 43 stress 5.03596e-05
## ... Procrustes: rmse 0.226756 max resid 0.2709706
## Run 44 stress 0
## ... Procrustes: rmse 0.1308585 max resid 0.1865175
## Run 45 stress 0
## ... Procrustes: rmse 0.2285948 max resid 0.4096774
## Run 46 stress 0
## ... Procrustes: rmse 0.2375731 max resid 0.3947861
## Run 47 stress 8.016021e-05
## ... Procrustes: rmse 0.2294485 max resid 0.4029602
## Run 48 stress 9.958433e-05
## ... Procrustes: rmse 0.1623946 max resid 0.265649
## Run 49 stress 0
## ... Procrustes: rmse 0.07481238 max resid 0.11158
## Run 50 stress 4.471901e-05
## ... Procrustes: rmse 0.03892019 max resid 0.05417969
## Run 51 stress 8.715565e-05
## ... Procrustes: rmse 0.2300562 max resid 0.30818
## Run 52 stress 0
## ... Procrustes: rmse 0.08511088 max resid 0.151068
## Run 53 stress 0
## ... Procrustes: rmse 0.2180165 max resid 0.3636724
## Run 54 stress 0
## ... Procrustes: rmse 0.1763519 max resid 0.2955852
## Run 55 stress 6.789788e-05
## ... Procrustes: rmse 0.1361742 max resid 0.1800913
## Run 56 stress 0
## ... Procrustes: rmse 0.1431829 max resid 0.2190628
## Run 57 stress 0
## ... Procrustes: rmse 0.1594864 max resid 0.2155361
## Run 58 stress 0
## ... Procrustes: rmse 0.2005132 max resid 0.3524586
## Run 59 stress 0
## ... Procrustes: rmse 0.165439 max resid 0.1974747
## Run 60 stress 0
## ... Procrustes: rmse 0.09497237 max resid 0.1525758
## Run 61 stress 9.280306e-05
## ... Procrustes: rmse 0.2259055 max resid 0.4013282
## Run 62 stress 2.43618e-05
## ... Procrustes: rmse 0.09564025 max resid 0.1234208
## Run 63 stress 9.240547e-05
## ... Procrustes: rmse 0.1723737 max resid 0.308795
## Run 64 stress 0
## ... Procrustes: rmse 0.07759072 max resid 0.1100485
## Run 65 stress 0
## ... Procrustes: rmse 0.2008711 max resid 0.3765499
## Run 66 stress 0
## ... Procrustes: rmse 0.1895162 max resid 0.3271299
## Run 67 stress 0
## ... Procrustes: rmse 0.1957091 max resid 0.3944642
## Run 68 stress 8.97237e-05
## ... Procrustes: rmse 0.134721 max resid 0.2008305
## Run 69 stress 0
## ... Procrustes: rmse 0.1405048 max resid 0.2502531
## Run 70 stress 0
## ... Procrustes: rmse 0.2011602 max resid 0.2823315
## Run 71 stress 5.166469e-05
## ... Procrustes: rmse 0.08041961 max resid 0.1221728
## Run 72 stress 0
## ... Procrustes: rmse 0.2087462 max resid 0.3323884
## Run 73 stress 0
## ... Procrustes: rmse 0.1605193 max resid 0.2681912
## Run 74 stress 9.533563e-05
## ... Procrustes: rmse 0.1845128 max resid 0.2922687
## Run 75 stress 7.458746e-05
## ... Procrustes: rmse 0.1716324 max resid 0.2315354
## Run 76 stress 0.1512494
## Run 77 stress 9.886174e-05
## ... Procrustes: rmse 0.1384755 max resid 0.2417798
## Run 78 stress 0
## ... Procrustes: rmse 0.1214548 max resid 0.1679333
## Run 79 stress 0.1512494
## Run 80 stress 6.811102e-05
## ... Procrustes: rmse 0.1422093 max resid 0.2429922
## Run 81 stress 8.087179e-05
## ... Procrustes: rmse 0.1542973 max resid 0.2198985
## Run 82 stress 8.625092e-05
## ... Procrustes: rmse 0.2434134 max resid 0.440316
## Run 83 stress 0
## ... Procrustes: rmse 0.2358538 max resid 0.4260843
## Run 84 stress 7.314124e-05
## ... Procrustes: rmse 0.1208427 max resid 0.1643601
## Run 85 stress 9.443833e-05
## ... Procrustes: rmse 0.2304085 max resid 0.4253988
## Run 86 stress 3.64926e-05
## ... Procrustes: rmse 0.1465787 max resid 0.2140089
## Run 87 stress 0
## ... Procrustes: rmse 0.09510719 max resid 0.1248787
## Run 88 stress 0
## ... Procrustes: rmse 0.237263 max resid 0.3521101
## Run 89 stress 9.093125e-05
## ... Procrustes: rmse 0.1254003 max resid 0.1743458
## Run 90 stress 0
## ... Procrustes: rmse 0.1769971 max resid 0.3197116
## Run 91 stress 0
## ... Procrustes: rmse 0.04310136 max resid 0.06127615
## *** No convergence -- monoMDS stopping criteria:
## 88: stress < smin
## 2: stress ratio > sratmax
## 1: scale factor of the gradient < sfgrmin
## [1] "No Convergence"
| Group1 | Group2 | Group3 | Group4 | Group5 |
|---|---|---|---|---|
| vAMPtest_AminoType1 | vAMPtest_AminoType10 | vAMPtest_AminoType7 | vAMPtest_AminoType16 | vAMPtest_AminoType11 |
| vAMPtest_AminoType13 | vAMPtest_AminoType12 | vAMPtest_AminoType8 | vAMPtest_AminoType3 | |
| vAMPtest_AminoType14 | vAMPtest_AminoType15 | |||
| vAMPtest_AminoType2 | vAMPtest_AminoType4 | |||
| vAMPtest_AminoType5 | vAMPtest_AminoType9 | |||
| vAMPtest_AminoType6 |
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(shannonaov)
## W = 0.92677, p-value = 0.5554
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 2.0493, df = 1, p-value = 0.1523
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.00181 0.00181 0.043 0.846
## Residuals 4 0.16991 0.04248
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = shannondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.03477559 -0.5019946 0.4324434 0.8463728
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(simpsonaov)
## W = 0.90983, p-value = 0.4353
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 2.52, df = 1, p-value = 0.1124
##
##
## --------------------------------------------------------------
##
## [1] "ANOVA Results"
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.00204 0.002037 0.111 0.756
## Residuals 4 0.07336 0.018339
##
## --------------------------------------------------------------
##
## [1] "Tukey HSD - Pairwise comparison - significant differences indicated by p-value < 0.05"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = index ~ treatment, data = simpsondata5_2)
##
## $treatment
## diff lwr upr p adj
## Group2-Group1 -0.03685422 -0.3438498 0.2701413 0.7556408
##
##
## --------------------------------------------------------------
## [1] "Shapiro Test of normality - data is normal if p-value > 0.05"
##
## Shapiro-Wilk normality test
##
## data: resid(richaov)
## W = 0.83508, p-value = 0.1186
##
##
## --------------------------------------------------------------
##
## [1] "Bartlett Test variance homogeneity - variance is homogeneous if p-value > 0.05"
##
## Bartlett test of homogeneity of variances
##
## data: index by treatment
## Bartlett's K-squared = 21.019, df = 1, p-value = 4.547e-06
##
##
## --------------------------------------------------------------
##
## [1] "Data either not normal or variance not homogenous"
## [1] "Kruskal-Wallis Test - test significant if p <.05"
##
## Kruskal-Wallis rank sum test
##
## data: index by treatment
## Kruskal-Wallis chi-squared = 0.42857, df = 1, p-value = 0.5127
##
##
## --------------------------------------------------------------
##
## [1] "Data not significant. Skipping pairwise comparison"
##
## --------------------------------------------------------------
##
## [1] "ANOVA - one or more of the assumptions not met, take with a grain of salt."
## Df Sum Sq Mean Sq F value Pr(>F)
## treatment 1 0.5141 0.5141 2.342 0.201
## Residuals 4 0.8778 0.2195
##
## --------------------------------------------------------------
##
## Call:
## adonis(formula = bray.distance ~ meddata5$treatment)
##
## Permutation: free
## Number of permutations: 719
##
## Terms added sequentially (first to last)
##
## Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
## meddata5$treatment 1 0.72083 0.72083 13.455 0.77084 0.1
## Residuals 4 0.21430 0.05357 0.22916
## Total 5 0.93513 1.00000
## Run 0 stress 0
## Run 1 stress 9.585412e-05
## ... Procrustes: rmse 0.07327924 max resid 0.1089457
## Run 2 stress 9.857982e-05
## ... Procrustes: rmse 0.1270674 max resid 0.2463404
## Run 3 stress 9.861741e-05
## ... Procrustes: rmse 0.1502306 max resid 0.2849561
## Run 4 stress 0
## ... Procrustes: rmse 0.1801679 max resid 0.3507864
## Run 5 stress 9.751848e-05
## ... Procrustes: rmse 0.07208713 max resid 0.1296016
## Run 6 stress 0
## ... Procrustes: rmse 0.05254968 max resid 0.1146751
## Run 7 stress 9.328431e-05
## ... Procrustes: rmse 0.07734704 max resid 0.1424702
## Run 8 stress 0.2475416
## Run 9 stress 0
## ... Procrustes: rmse 0.1868644 max resid 0.3632897
## Run 10 stress 8.874472e-05
## ... Procrustes: rmse 0.07841869 max resid 0.1244634
## Run 11 stress 9.802216e-05
## ... Procrustes: rmse 0.1582175 max resid 0.2170241
## Run 12 stress 0
## ... Procrustes: rmse 0.09463104 max resid 0.1394922
## Run 13 stress 9.999985e-05
## ... Procrustes: rmse 0.1485101 max resid 0.2708957
## Run 14 stress 9.712869e-05
## ... Procrustes: rmse 0.1243946 max resid 0.2448997
## Run 15 stress 9.426449e-05
## ... Procrustes: rmse 0.1405494 max resid 0.2029695
## Run 16 stress 7.305698e-05
## ... Procrustes: rmse 0.08175434 max resid 0.1129446
## Run 17 stress 9.946186e-05
## ... Procrustes: rmse 0.06873862 max resid 0.1051037
## Run 18 stress 7.610085e-05
## ... Procrustes: rmse 0.1413648 max resid 0.2653288
## Run 19 stress 9.858073e-05
## ... Procrustes: rmse 0.1755062 max resid 0.3409782
## Run 20 stress 9.456826e-05
## ... Procrustes: rmse 0.1347099 max resid 0.2386779
## Run 21 stress 9.183441e-05
## ... Procrustes: rmse 0.1258241 max resid 0.2476287
## Run 22 stress 0
## ... Procrustes: rmse 0.1532964 max resid 0.3114371
## Run 23 stress 5.756077e-05
## ... Procrustes: rmse 0.07489994 max resid 0.1093775
## Run 24 stress 0
## ... Procrustes: rmse 0.1401128 max resid 0.2620271
## Run 25 stress 9.887306e-05
## ... Procrustes: rmse 0.03401171 max resid 0.04746078
## Run 26 stress 7.080787e-05
## ... Procrustes: rmse 0.08441362 max resid 0.1380451
## Run 27 stress 4.617498e-05
## ... Procrustes: rmse 0.0960515 max resid 0.1432842
## Run 28 stress 0.2181459
## Run 29 stress 0.1420473
## Run 30 stress 9.910669e-05
## ... Procrustes: rmse 0.1468215 max resid 0.2834265
## Run 31 stress 0.2181459
## Run 32 stress 1.686234e-05
## ... Procrustes: rmse 0.09406121 max resid 0.1953348
## Run 33 stress 6.999688e-06
## ... Procrustes: rmse 0.1514338 max resid 0.2838615
## Run 34 stress 9.989874e-05
## ... Procrustes: rmse 0.1043052 max resid 0.1800418
## Run 35 stress 0.2181459
## Run 36 stress 7.031922e-05
## ... Procrustes: rmse 0.1358158 max resid 0.2834797
## Run 37 stress 9.93899e-05
## ... Procrustes: rmse 0.1350616 max resid 0.2565868
## Run 38 stress 8.927707e-05
## ... Procrustes: rmse 0.1458258 max resid 0.2069644
## Run 39 stress 8.952397e-05
## ... Procrustes: rmse 0.1362748 max resid 0.2540981
## Run 40 stress 0.2181459
## Run 41 stress 0.2181459
## Run 42 stress 9.759003e-05
## ... Procrustes: rmse 0.1634158 max resid 0.2746343
## Run 43 stress 0.2181459
## Run 44 stress 0.2181459
## Run 45 stress 9.87518e-05
## ... Procrustes: rmse 0.1457379 max resid 0.2066602
## Run 46 stress 9.046244e-05
## ... Procrustes: rmse 0.1337007 max resid 0.25568
## Run 47 stress 9.998735e-05
## ... Procrustes: rmse 0.04981747 max resid 0.07810493
## Run 48 stress 9.980543e-05
## ... Procrustes: rmse 0.1272336 max resid 0.2487549
## Run 49 stress 0.2181459
## Run 50 stress 0.2673072
## Run 51 stress 9.993578e-05
## ... Procrustes: rmse 0.09695027 max resid 0.1444623
## Run 52 stress 0.2673072
## Run 53 stress 0.000134598
## ... Procrustes: rmse 0.1101945 max resid 0.1854303
## Run 54 stress 9.907934e-05
## ... Procrustes: rmse 0.1497929 max resid 0.2751593
## Run 55 stress 9.946331e-05
## ... Procrustes: rmse 0.08546929 max resid 0.1464614
## Run 56 stress 6.777974e-05
## ... Procrustes: rmse 0.07446326 max resid 0.1086965
## Run 57 stress 9.996264e-05
## ... Procrustes: rmse 0.09074312 max resid 0.1343754
## Run 58 stress 0.2181459
## Run 59 stress 9.719748e-05
## ... Procrustes: rmse 0.1128387 max resid 0.2188887
## Run 60 stress 1.065671e-05
## ... Procrustes: rmse 0.1099643 max resid 0.221548
## Run 61 stress 5.878816e-05
## ... Procrustes: rmse 0.1446279 max resid 0.2607854
## Run 62 stress 0
## ... Procrustes: rmse 0.1256665 max resid 0.2642728
## Run 63 stress 9.918995e-05
## ... Procrustes: rmse 0.1403145 max resid 0.2776022
## Run 64 stress 9.7122e-05
## ... Procrustes: rmse 0.1434446 max resid 0.2727137
## Run 65 stress 9.157868e-05
## ... Procrustes: rmse 0.1097596 max resid 0.179497
## Run 66 stress 9.93306e-05
## ... Procrustes: rmse 0.1234979 max resid 0.1758401
## Run 67 stress 8.919613e-05
## ... Procrustes: rmse 0.128694 max resid 0.2334423
## Run 68 stress 9.985828e-05
## ... Procrustes: rmse 0.1466615 max resid 0.2288707
## Run 69 stress 0.2673072
## Run 70 stress 2.793785e-05
## ... Procrustes: rmse 0.1506661 max resid 0.2819387
## Run 71 stress 7.619131e-05
## ... Procrustes: rmse 0.1444494 max resid 0.276718
## Run 72 stress 0.2673072
## Run 73 stress 7.984382e-05
## ... Procrustes: rmse 0.1552394 max resid 0.2859154
## Run 74 stress 0
## ... Procrustes: rmse 0.1140415 max resid 0.2347693
## Run 75 stress 7.725195e-05
## ... Procrustes: rmse 0.1857908 max resid 0.3160335
## Run 76 stress 9.95308e-05
## ... Procrustes: rmse 0.08300283 max resid 0.1577888
## Run 77 stress 8.805808e-05
## ... Procrustes: rmse 0.1346856 max resid 0.238693
## Run 78 stress 0.2269841
## Run 79 stress 9.647378e-05
## ... Procrustes: rmse 0.1434534 max resid 0.2054263
## Run 80 stress 0
## ... Procrustes: rmse 0.1227926 max resid 0.2340298
## Run 81 stress 9.995321e-05
## ... Procrustes: rmse 0.200892 max resid 0.3686475
## Run 82 stress 9.978573e-05
## ... Procrustes: rmse 0.1080433 max resid 0.199099
## Run 83 stress 9.893066e-05
## ... Procrustes: rmse 0.1641548 max resid 0.3152901
## Run 84 stress 9.825552e-05
## ... Procrustes: rmse 0.1333982 max resid 0.1959094
## Run 85 stress 9.997688e-05
## ... Procrustes: rmse 0.1389627 max resid 0.2597169
## Run 86 stress 9.331601e-05
## ... Procrustes: rmse 0.1560821 max resid 0.215252
## Run 87 stress 9.928466e-05
## ... Procrustes: rmse 0.1461129 max resid 0.207274
## Run 88 stress 0
## ... Procrustes: rmse 0.08178748 max resid 0.1136605
## Run 89 stress 9.776469e-05
## ... Procrustes: rmse 0.1284732 max resid 0.2447713
## Run 90 stress 0.1420473
## Run 91 stress 9.999834e-05
## ... Procrustes: rmse 0.1713422 max resid 0.3100415
## *** No convergence -- monoMDS stopping criteria:
## 1: no. of iterations >= maxit
## 73: stress < smin
## 5: stress ratio > sratmax
## 12: scale factor of the gradient < sfgrmin
## [1] "No Convergence"
## Run 0 stress 0
## Run 1 stress 9.746115e-05
## ... Procrustes: rmse 0.1794925 max resid 0.2554082
## Run 2 stress 9.726057e-05
## ... Procrustes: rmse 0.09336036 max resid 0.112527
## Run 3 stress 0
## ... Procrustes: rmse 0.1845616 max resid 0.261067
## Run 4 stress 9.811586e-05
## ... Procrustes: rmse 0.1654116 max resid 0.2377823
## Run 5 stress 9.897519e-05
## ... Procrustes: rmse 0.1636414 max resid 0.315313
## Run 6 stress 9.905148e-05
## ... Procrustes: rmse 0.1247494 max resid 0.143512
## Run 7 stress 9.038443e-05
## ... Procrustes: rmse 0.2412218 max resid 0.3562837
## Run 8 stress 0
## ... Procrustes: rmse 0.2392688 max resid 0.356421
## Run 9 stress 9.740945e-05
## ... Procrustes: rmse 0.1264608 max resid 0.1927137
## Run 10 stress 9.656648e-05
## ... Procrustes: rmse 0.2238776 max resid 0.3423013
## Run 11 stress 0
## ... Procrustes: rmse 0.2068343 max resid 0.291535
## Run 12 stress 1.887865e-06
## ... Procrustes: rmse 0.2289719 max resid 0.3418164
## Run 13 stress 0
## ... Procrustes: rmse 0.1833294 max resid 0.290401
## Run 14 stress 0
## ... Procrustes: rmse 0.2369303 max resid 0.3563845
## Run 15 stress 9.109824e-05
## ... Procrustes: rmse 0.1728675 max resid 0.3197143
## Run 16 stress 0
## ... Procrustes: rmse 0.2229369 max resid 0.3374696
## Run 17 stress 8.290753e-05
## ... Procrustes: rmse 0.1246337 max resid 0.1510449
## Run 18 stress 9.944355e-05
## ... Procrustes: rmse 0.1973032 max resid 0.3080051
## Run 19 stress 8.083138e-05
## ... Procrustes: rmse 0.2290339 max resid 0.3520068
## Run 20 stress 6.792144e-05
## ... Procrustes: rmse 0.1674355 max resid 0.2190931
## Run 21 stress 9.528436e-05
## ... Procrustes: rmse 0.2055821 max resid 0.2979368
## Run 22 stress 8.075265e-05
## ... Procrustes: rmse 0.2223715 max resid 0.2711622
## Run 23 stress 0
## ... Procrustes: rmse 0.1817135 max resid 0.2571223
## Run 24 stress 9.6965e-05
## ... Procrustes: rmse 0.2245289 max resid 0.3488218
## Run 25 stress 9.603039e-05
## ... Procrustes: rmse 0.2555124 max resid 0.3696133
## Run 26 stress 9.923892e-05
## ... Procrustes: rmse 0.1156229 max resid 0.1503739
## Run 27 stress 8.609133e-05
## ... Procrustes: rmse 0.139489 max resid 0.2338511
## Run 28 stress 8.894788e-05
## ... Procrustes: rmse 0.1910622 max resid 0.3252138
## Run 29 stress 4.585002e-05
## ... Procrustes: rmse 0.2515775 max resid 0.34437
## Run 30 stress 8.491532e-05
## ... Procrustes: rmse 0.1831631 max resid 0.2346807
## Run 31 stress 9.974779e-05
## ... Procrustes: rmse 0.1204997 max resid 0.2189615
## Run 32 stress 9.691362e-05
## ... Procrustes: rmse 0.229504 max resid 0.3500407
## Run 33 stress 6.385353e-05
## ... Procrustes: rmse 0.2333178 max resid 0.3463476
## Run 34 stress 6.783829e-05
## ... Procrustes: rmse 0.1463079 max resid 0.1961894
## Run 35 stress 0
## ... Procrustes: rmse 0.1475202 max resid 0.2459833
## Run 36 stress 0
## ... Procrustes: rmse 0.1865431 max resid 0.2479839
## Run 37 stress 9.483871e-05
## ... Procrustes: rmse 0.1761117 max resid 0.3146322
## Run 38 stress 2.104829e-06
## ... Procrustes: rmse 0.1867573 max resid 0.3334097
## Run 39 stress 9.997529e-05
## ... Procrustes: rmse 0.2149516 max resid 0.3321053
## Run 40 stress 5.295879e-05
## ... Procrustes: rmse 0.2167892 max resid 0.3151854
## Run 41 stress 9.646146e-05
## ... Procrustes: rmse 0.2137914 max resid 0.3633107
## Run 42 stress 6.275657e-05
## ... Procrustes: rmse 0.1199679 max resid 0.160565
## Run 43 stress 9.545984e-05
## ... Procrustes: rmse 0.04180981 max resid 0.07187198
## Run 44 stress 7.542458e-05
## ... Procrustes: rmse 0.1997764 max resid 0.2482091
## Run 45 stress 9.905097e-05
## ... Procrustes: rmse 0.1352612 max resid 0.2146732
## Run 46 stress 9.667386e-05
## ... Procrustes: rmse 0.2231514 max resid 0.3419346
## Run 47 stress 0
## ... Procrustes: rmse 0.1945145 max resid 0.271751
## Run 48 stress 9.950043e-05
## ... Procrustes: rmse 0.1863854 max resid 0.3237835
## Run 49 stress 9.801513e-05
## ... Procrustes: rmse 0.2416272 max resid 0.3665619
## Run 50 stress 7.348622e-05
## ... Procrustes: rmse 0.2576533 max resid 0.3622165
## Run 51 stress 9.871815e-05
## ... Procrustes: rmse 0.1711456 max resid 0.2931756
## Run 52 stress 0
## ... Procrustes: rmse 0.1568618 max resid 0.2144868
## Run 53 stress 6.171768e-05
## ... Procrustes: rmse 0.2467415 max resid 0.3323091
## Run 54 stress 9.02198e-05
## ... Procrustes: rmse 0.1655323 max resid 0.270452
## Run 55 stress 9.717595e-05
## ... Procrustes: rmse 0.188402 max resid 0.3248317
## Run 56 stress 9.970836e-05
## ... Procrustes: rmse 0.2418892 max resid 0.3688925
## Run 57 stress 8.883428e-05
## ... Procrustes: rmse 0.2431958 max resid 0.3358697
## Run 58 stress 8.450146e-05
## ... Procrustes: rmse 0.2307265 max resid 0.3272124
## Run 59 stress 0
## ... Procrustes: rmse 0.1779714 max resid 0.2597214
## Run 60 stress 0
## ... Procrustes: rmse 0.1472528 max resid 0.2282055
## Run 61 stress 0.1275225
## Run 62 stress 8.067923e-05
## ... Procrustes: rmse 0.2379497 max resid 0.3672265
## Run 63 stress 2.710865e-05
## ... Procrustes: rmse 0.2462116 max resid 0.3859162
## Run 64 stress 4.979447e-05
## ... Procrustes: rmse 0.2134418 max resid 0.3177205
## Run 65 stress 9.378711e-05
## ... Procrustes: rmse 0.1764649 max resid 0.3293835
## Run 66 stress 8.716384e-05
## ... Procrustes: rmse 0.1996285 max resid 0.2811454
## Run 67 stress 9.06816e-05
## ... Procrustes: rmse 0.2476572 max resid 0.3705361
## Run 68 stress 7.708894e-05
## ... Procrustes: rmse 0.1088011 max resid 0.2109173
## Run 69 stress 8.380303e-05
## ... Procrustes: rmse 0.1984961 max resid 0.2781993
## Run 70 stress 0.1512494
## Run 71 stress 9.203062e-05
## ... Procrustes: rmse 0.1605292 max resid 0.2669709
## Run 72 stress 7.079012e-05
## ... Procrustes: rmse 0.2458423 max resid 0.3462206
## Run 73 stress 0
## ... Procrustes: rmse 0.199538 max resid 0.3328155
## Run 74 stress 5.375749e-07
## ... Procrustes: rmse 0.1884324 max resid 0.2799996
## Run 75 stress 0.1275227
## Run 76 stress 0
## ... Procrustes: rmse 0.1816124 max resid 0.2437729
## Run 77 stress 9.811146e-05
## ... Procrustes: rmse 0.2256537 max resid 0.2778362
## Run 78 stress 1.100064e-05
## ... Procrustes: rmse 0.2527877 max resid 0.3396898
## Run 79 stress 0
## ... Procrustes: rmse 0.2313656 max resid 0.3294618
## Run 80 stress 0
## ... Procrustes: rmse 0.1932941 max resid 0.3496722
## Run 81 stress 9.89386e-05
## ... Procrustes: rmse 0.1193919 max resid 0.1825183
## Run 82 stress 9.932087e-05
## ... Procrustes: rmse 0.1225201 max resid 0.2318763
## Run 83 stress 0.0001074903
## ... Procrustes: rmse 0.1753572 max resid 0.3213585
## Run 84 stress 0
## ... Procrustes: rmse 0.1416524 max resid 0.2579267
## Run 85 stress 0.1275226
## Run 86 stress 8.237454e-05
## ... Procrustes: rmse 0.1667862 max resid 0.3144216
## Run 87 stress 9.826993e-05
## ... Procrustes: rmse 0.18058 max resid 0.2943438
## Run 88 stress 9.824521e-05
## ... Procrustes: rmse 0.1331463 max resid 0.2114605
## Run 89 stress 0
## ... Procrustes: rmse 0.2135035 max resid 0.2604271
## Run 90 stress 1.094076e-05
## ... Procrustes: rmse 0.2537825 max resid 0.3472056
## Run 91 stress 8.326869e-06
## ... Procrustes: rmse 0.2253727 max resid 0.2779884
## *** No convergence -- monoMDS stopping criteria:
## 1: no. of iterations >= maxit
## 86: stress < smin
## 3: stress ratio > sratmax
## 1: scale factor of the gradient < sfgrmin
## [1] "No Convergence"